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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtcaacctaatcttaacatgtttatcatgccgattgcaaactgtgaagctcttttttttatatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG

Basic information

species Zea mays
transcript GRMZM2G011068_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011068_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g44590.2 (Oryza sativa), 3'ss of exon 2
gtaaatgtcaac-ctaatcttaacatg---tttatcatgccgattgcaaac----tgtgaagctcttttttttatatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG
|||||||||  | |||  |||   ||    | | | |||| ||| | |||     ||| |      | ||| | | ||||||||||||||| ||||| |||||| ||||| |||| |||||||||||||||||||||| |||||||||| | ||||||||||
gtaaatgtcctcgctatccttgctatatgatgtttgatgctgatagaaaagaaagtgtaataagactctttatgtgtcactcagAGGTTGATGATACACGGGGTCGAGTTTCTCTCTTAGATGGTGGCACAATCCTCAGCTTGCCAATGCTATATCTTCAAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211144537|gb|FL166805.1|FL166805
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71766061|gb|DR963998.1|DR963998
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211143112|gb|FL166799.1|FL166799
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144535|gb|FL166803.1|FL166803
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71448594|gb|DR829644.1|DR829644
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|71436330|gb|DR817380.1|DR817380
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|31664610|gb|CD573543.1|CD573543
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211143111|gb|FL166798.1|FL166798
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144538|gb|FL166806.1|FL166806
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144536|gb|FL166804.1|FL166804
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACGATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144532|gb|FL166800.1|FL166800
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|211144533|gb|FL166801.1|FL166801
EST:     CCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATANCCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATC
genomic: CCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATA-CCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATC
EST: gi|211143110|gb|FL166797.1|FL166797
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
EST: gi|76288774|gb|DV028342.1|DV028342
EST:     ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCG                         AGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC
genomic: ACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 76

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 55

AGATAACAATGGAGATGGAGTGGCTAGCACCTCTGGACCATTCACATTCAATAGGTCTCTAGCTTCACTGCACACATACCTTGGCGgtaaatgtca ... tatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtttatcatgccgattgcaaactgtgaagctcttttttttatatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG
 tcttaac  putative branch site (score: 55)
                                 ctcttttttttatatc  putative PPT
                                  tcttttttttatatca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtcaacctaatcttaacatgtttatcatgccgattgcaaactgtgaagctcttttttttatatcactcagAGGTTGACGATACTCGGGGTAGAGTTACTCTTTTAGATGGTGGCACAATCCTCAACTTGCCAATGTTTTATCTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG